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uses: Digest::MD5; File::Copy Term::ANSIColor; gfortran, wget, 7z, unzip ################################ CHANGES IN PRE-BETA (V0.0.8) ################################ * some bugs and inconsistencies fixed, further code cleaning ################################ CHANGES IN PRE-BETA (V0.0.7) ################################ * Implemented parallel SIGMA processing using Peter Valdemar Morch's Parallel::Loops module. http://search.cpan.org/~pmorch/Parallel-Loops/lib/Parallel/Loops.pm THIS IS NOT A DEFAULT PERL MODULE, you need to install it for the new feature to work properly! -> Scaling for small molecules is bad, but for biomolecules significant speed-up is achieved. * The random integer seed used in mobcal.run files can be fetched from www.random.org automatically. Thereby, the random number integer seed for the MOBCAL randomizer routines can be generated from atmospheric noise, instead of using a pseudo-randomizer to seed a pseudo-randomizer. * A feature was incorporated that enables the subsequent interfacing of modified MOBCAL executables. It is still in its infancy. * The CLI interface has been improved. The "noav" option now supports a fourth argument, thereby enabling the use of commands like [perl mobcalPARSER.pl noav input.xyz xyz none output.mfj], whereby sets of input files can be parsed using external scripts. * The adjustments that can be made to mobcal.f were extended, an option to inject Lennard-Jones parameters for elements not included in the original source was incorporated. * The CLI argument "L" now calls the license, whereas "C" opens a list of relevant publications in the browser (works only under windows). * Code cleaning, simplifications and improved documentation. ################################ CHANGES IN PRE-BETA (V0.0.6) ################################ * PDB support has been improved. * MOBCAL is downloaded automatically under Linux. * Improved user support under Windows. * improved logging routine (citations etc.). * several bug-fixes ################################ CHANGES IN PRE-BETA (V0.0.5) ################################ * XYZ parsing has been improved, TINKER xyz format is now automatically detected and parsed. http://dasher.wustl.edu/tinker/ * rudimentary NWChem (ver. 4.7, 4.6 does not work) support added: http://www.nwchem-sw.org/index.php/Main_Page * logfile feature added * support for 4 character file extensions added * started code cleaning and simplification * minor bugfixes concerning corrupted screen output * mayor bugfix concerning the extraction of loewdin charges from ORCA output. ################################ CHANGES IN PRE-BETA (V0.0.4) ################################ * Support for Jaguar output was implemented. Extraction of charge analysis data is not yet fully supported (tested Jaguar version 5.0, release 22). ADDITIONAL BUGFIXES: Support for SIGMA now works under linux (Ubuntu 12.04 64bit tested, cf. changes in v0.0.3). * I corrected some typos and added automatic OS recognition. However, there might be some bugs I did not come across. Additionally, I tested the script under Win64 using Strawberry Perl (v5.16.11) without problems. http://strawberryperl.com/ * I did not test compatibility to Orca 2.9.1 yet, this on the todo-list for v0.0.5. http://www.mpibac.mpg.de/bac/logins/neese/description.php ################################ CHANGES IN PRE-BETA (v0.0.3) ################################ *SIGMA: The SIGMA program from the Bowers group is now also supported, but was only tested properly under win32. SIGMA can be obtained from Thomas Wyttenbach. For details see: http://bowers.chem.ucsb.edu/theory_analysis/cross-sections/index.shtml citations: von Helden, G.; Hsu, M.-T.; Gotts, N.; Bowers, M. T. J. Phys. Chem. 1993, 97, 8182-8192. Wyttenbach, T.; von Helden, G.; Batka, J. J., Jr.; Carlat, D.; Bowers, M. T. J. Am. Soc. Mass Spectrom. 1997, 8, 275-282. Wyttenbach, T.; Witt, M.; Bowers, M. T. J. Am. Chem. Soc. 2000, 122, 3458-3464. To use SIGMA in conjunction with mobcalPARSER, you need to obtain the SIGMA source code from Thomas Wyttenbach, compile it using e.g. gfortran -std=legacy, rename the new binary to "sigma.exe" and place it in your mobcalPARSER directory together with the parameter files you get packaged with the SIGMA source. mobcalPARSER only calls the "ion size scaled Lennard-Jones" model, since the other two are already available in MOBCAL. If you do not want to use SIGMA, you do not have to do anything. The program checks whether "sigma.exe" is present and overrides to mobcal execution when "sigma.exe" is not found in the working directory. Under Linux, you can try to rename your compiled SIGMA binary to "sigma.exe" this should work in general, however, this feature is not yet fully tested under Linux. Alternatively the mobcalPARSER source code can be modified in line 1200. Simply remove the ".exe" file extension from the execution command. ################################ CHANGES IN PRE-BETA (v0.0.2) ################################ *LINUX: config.cfg differs from v0.0.1, inserting "./mobcal" doesn't work anymore, replace "mobcal.exe" by "mobcal" in the new version! *minor bugfixes and typo corrections... *added "assisted MOBCAL compilation": If you do not want to use this feature, simply do not place any file called "mobcal.f" in working directory, or use command line options. The original MOBCAL source code (junko.f build) is preconfigured for multiple geometry input and NOT FOR DEFAULT single geometry input. mobcalPARSER v0.0.2 offers to modify the source and adjust the settings to default values, the modified source is automatically compiled afterwards using gfortran. The binary is removed in the end, but the modified source is stored in the output directory, the original source is NOT modified. Once you have found settings that suit your purpose you can compile custom.f manually, remove mobcal.f from working directory and put your custom mobcal.exe in the working directory. Details: Several adjustments are possible, recommended settings are preselected using [UC/lc] syntax (Upper Case means 'recommended'). MOBCAL source allows lots of additional modifications, I didn't add all of them to the script. By default AMC extends the MOBCAL output format by the initial coordinates and charges read by FCOORD, you can check whether or not your input was passed through correctly by comparing to your initial input. The feature requires installed gfortran (add to PATH variable), under Win32 you can use MinGW (http://sourceforge.net/projects/mingw/files/). ################################ GENERAL RELEASE NOTES ################################ "MOBCAL - A Program to Calculate Mobilities" is the intellectual property of Professor Martin F. Jarrold. The fortran77 source code is available free of charge at http://www.indiana.edu/~nano/software.html. citations: M. F. Mesleh, J. M. Hunter, A. A. Shvartsburg, G. C. Schatz and M. F. Jarrold, J. Phys. Chem. 1996, 100, 16082-16086; Erratum, J. Phys. Chem. A 1997, 101, 968. A. A. Shvartsburg and M. F. Jarrold, Chem. Phys. Lett. 1996, 261, 86-91. mobcalPARSER is a PERL frontend, the original MOBCAL fortran77 code is not contained in the standard package (cf. "artistic license"), you can download the source from the address provided above (build 06/15/00). To compile MOBCAL you can use e.g. Force 2.0.9 (win32) or gfortran (-std=legacy). mobcalPARSER v0.0.1 was tested in combination with: > Orca 2.7.0 & 2.8.0; > Gaussian 94, 98, 03 & 09; > .xyz and .mol The frontend runs on linux and win32, but it's preconfigured for win32. Under linux you have to change config.cfg. There is a line initially called 'mobcal.exe", change it to "mobcal", where "mobcal" is the compiled MOBCAL program (use chmod +x ..). This is EXPERIMENTAL SOFTWARE and COMES WITH ABSOLUTELY NO WARRANTY, read the license (license is present in source and printed on screen when you run the frontend for the first time, set 'c' switch to read it on screen later on). == AUTOMATIC PROCESSING ================================================== By default (i.e. calling the script without switches) files in the working directory are processed automatically. You can simply copy the file(s) you want to pass through into the working directory and run the program by 'double-clicking' mobcalPARSER.pl. The following hierarchy applies for automatic processing: > *.out FILES ARE TREATED AS ORCA OUTPUT > *.log FILES ARE TREATED AS GAUSSIAN OUTPUT > *.xyz FILES ARE TREATED AS XYZ GEOMETRY > *.mol FILES ARE TREATED AS MDL MOL GEOMETRY Therefore, .log files are ignored as long as .out files are present, while .xyz files are ignored as long as .log files are present. By default each file extension recognized is linked to a parsing subroutine (cf. above). When the script is called without command line arguments, the user is asked to enter the method of charge analysis manually (except *.xyz where no charge information is present, notations like [UC/lc] give UC on pressing return). When mobcal.exe is found in the working directory, the program is executed automatically. When finished, the MD5 checksum of mobcal.exe, as well as the mfj and run files are appended to the output file (*.mob). The MD5 checksum could later on be used to identify the MOBCAL build used to calculate the CCS and mobilities. In the end, a new directory is created where both the input (*.log or else) and the output (*.mob) are moved. == MULTI-GEOMETRY OUTPUT ================================================= Multiple files with one of the specified file extensions are treated as ISOMERS and appended to the same MOBCAL file. MOBCAL in turn uses this type of input to average the CCS of different isomers (rotamers). When converting multiple files, be sure not to accidently have files of the same file extension present in your working directory, as all files will be appended to the same hashes. Either rename or delete the files or use command line switches (scroll down). If the default settings are not suitable for your purposes, which could be the case if e.g. your gaussian files have a different file extension than *.log (e.g. *.g09) you may want to use command line switches (scroll down) or modify config.cfg. == CONFIGURATION FILE config.cfg ========================================= When the program is started for the first time, the user is asked, whether or not a new config.cfg file should be created. This status can be reset by deleting or renaming the config.cfg file in the working directory. MOBCAL recognizes different elements by their integer mass. However, by default MOBCAL uses the same parameters for heavier elements as for silicon. Each element that is found in your geometry file (ORCA, GAUSSIAN or else) has to be specified in the element table present in config.cfg. However, the integer mass you enter has to be present in MOBCAL source code, if it is not you can use a workaround (cf. config.cfg & MOBCAL code LINE 577 ff). You can also change the default file extensions used for automatic processing by changing the flag in line 4. Colored ANSI output can be enabled by setting the flag in line 6, this is not compatible to cmd.exe (Win32) by default. Jason Hood's ANSICON is capable of displaying ANSI escapes in Win32 (http://adoxa.3eeweb.com/ansicon/), which works with TERM::ANSIcolor package under Win32. It greatly improves the readability of the screen output, so it's worth the effort. == Protein Database Format (pdb) ========================================= A rudimentary support for *.pdb file parsing has been implemented in the beta release. However, this routine does not support actual protein database files. The support is limited to simple *.pdb files generated by certain molecular modelling software (e.g. Avogadro). == COMMAND LINE SWITCHES ================================================= SWITCHES OVERRIDE MOST OF THE FULLY AUTOMATIC PROCESSING ROUTINES. THE PASS THROUGH TO MOBCAL IS DISABLED TO ENABLE EXTERNAL ACCESS BY SCRIPTS. -- 1st EXAMPLE ----------------------------------------------------------- mobcalPARSER.pl cmd g09 gauss Calls the script to search for *.g09 files and parse them using the Gaussian routine (ORCA subroutine is called with 'orca'). The automatic file search routine is enabled when the cmd switch is used. -- 2nd EXAMPLE ----------------------------------------------------------- mobcalPARSER.pl noav example.g03 gauss mulliken 'noav' overrides automatic filesearch. The following switches call the script to parse the specified file (example.g03) with gaussian subroutine (gauss) using Mulliken charges (alternatively 'none' would override the charge analysis). noav overrides ALL automatic routines. The filename specified in line 2 of config.cfg contains the mobcal compatible input (mfj). == Artistic License ====================================================== This program comes with absolutely no warranty, the source code is licensed under the "Artistic License". This license is part of the source code and is displayed when the program is started for the first time by default. Type "mobcalPARSER.pl c" to view the license. This software comes with ABSOLUTELY NO WARRANTY. == KNOWN ISSUES ========================================================== <!> Special characters in file names are not displayed properly <!> remember to remove carriage returns (CR) when you copy modified config.cfg's from Win32 to Linux, if you forget, screen output gets partially corrupted! <!> BSD/Mac compatibility untested (on the to do list for BETA) ========================================================================== ========================== J.P. Boyd Dec 2012 =========================== ==========================================================================
Source: readme, updated 2012-12-22